The present study investigated the effects of an exercise intervention, which was implemented during school-break time, on the P300 component of event-related potentials and inhibitory control. Adolescents aged 12–15 years were allocated to an exercise and control group. The exercise group performed 20 min of aerobic and coordinative exercise per school day over a period of 8 weeks. Before and after the intervention, stimulus-locked event-related potentials were recorded during a Stroop task using electroencephalography. Cluster-based permutation testing revealed a greater increase of the P300 amplitude in the exercise compared to the control group, most pronounced for the parieto-occipital region. Additionally, increases in P300 amplitude were associated with decreases in incompatible reaction time on the Stroop task. An exercise program implemented during school-break time enhances adolescents' inhibitory control. This benefit seems to be due to an improved allocation of attentional resources towards the cognitive task.